New remote sensing sensors now acquire high spatial and spectral Satellite Image Time Series (SITS) of the world. These series of images are a key component of classification systems that aim at obtaining up-to-date and accurate land cover maps of the Earth's surfaces. More specifically, the combination of the temporal, spectral and spatial resolutions of new SITS makes possible to monitor vegetation dynamics. Although traditional classification algorithms, such as Random Forest (RF), have been successfully applied for SITS classification, these algorithms do not make the most of the temporal domain. Conversely, some approaches that take into account the temporal dimension have recently been tested, especially Recurrent Neural Networks (RNNs). This paper proposes an exhaustive study of another deep learning approaches, namely Temporal Convolutional Neural Networks (TempCNNs) where convolutions are applied in the temporal dimension. The goal is to quantitatively and qualitatively evaluate the contribution of TempCNNs for SITS classification. This paper proposes a set of experiments performed on one million time series extracted from 46 Formosat-2 images. The experimental results show that TempCNNs are more accurate than RF and RNNs, that are the current state of the art for SITS classification. We also highlight some differences with results obtained in computer vision, e.g. about pooling layers. Moreover, we provide some general guidelines on the network architecture, common regularization mechanisms, and hyper-parameter values such as batch size. Finally, we assess the visual quality of the land cover maps produced by TempCNNs.

With the explosive growth of biological sequences generated in the post-genomic era, one of the most challenging problems in bioinformatics and computational biology is to computationally characterize sequences, structures and functions in an efficient, accurate and high-throughput manner. A number of online web servers and stand-alone tools have been developed to address this to date; however, all these tools have their limitations and drawbacks in terms of their effectiveness, user-friendliness and capacity. Here, we present iLearn, a comprehensive and versatile Python-based toolkit, integrating the functionality of feature extraction, clustering, normalization, selection, dimensionality reduction, predictor construction, best descriptor/model selection, ensemble learning and results visualization for DNA, RNA and protein sequences. iLearn was designed for users that only want to upload their data set and select the functions they need calculated from it, while all necessary procedures and optimal settings are completed automatically by the software. iLearn includes a variety of descriptors for DNA, RNA and proteins, and four feature output formats are supported so as to facilitate direct output usage or communication with other computational tools. In total, iLearn encompasses 16 different types of feature clustering, selection, normalization and dimensionality reduction algorithms, and five commonly used machine-learning algorithms, thereby greatly facilitating feature analysis and predictor construction. iLearn is made freely available via an online web server and a stand-alone toolkit.

OPUS is a branch and bound search algorithm that enables efficient admissible search through spaces for which the order of search operator application is not significant. The algorithm's search efficiency is demonstrated with respect to very large machine learning search spaces. The use of admissible search is of potential value to the machine learning community as it means that the exact learning biases to be employed for complex learning tasks can be precisely specified and manipulated. OPUS also has potential for application in other areas of artificial intelligence, notably, truth maintenance.

Sequence-based analysis and prediction are fundamental bioinformatic tasks that facilitate understanding of the sequence(-structure)-function paradigm for DNAs, RNAs and proteins. Rapid accumulation of sequences requires equally pervasive development of new predictive models, which depends on the availability of effective tools that support these efforts. We introduce iLearnPlus, the first machine-learning platform with graphical- and web-based interfaces for the construction of machine-learning pipelines for analysis and predictions using nucleic acid and protein sequences. iLearnPlus provides a comprehensive set of algorithms and automates sequence-based feature extraction and analysis, construction and deployment of models, assessment of predictive performance, statistical analysis, and data visualization; all without programming. iLearnPlus includes a wide range of feature sets which encode information from the input sequences and over twenty machine-learning algorithms that cover several deep-learning approaches, outnumbering the current solutions by a wide margin. Our solution caters to experienced bioinformaticians, given the broad range of options, and biologists with no programming background, given the point-and-click interface and easy-to-follow design process. We showcase iLearnPlus with two case studies concerning prediction of long noncoding RNAs (lncRNAs) from RNA transcripts and prediction of crotonylation sites in protein chains. iLearnPlus is an open-source platform available at https://github.com/Superzchen/iLearnPlus/ with the webserver at http://ilearnplus.erc.monash.edu/.

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